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<p class="MsoNormal">I’m trying to run some scripts against the Ensembl perl API. I used to run these on a old server and I’ve now moved to a new one so I’m setting things up again.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve got all of the necessary Perl modules installed, but I can’t get the registry to load. Even a basic:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">my $registry = 'Bio::EnsEMBL::Registry';<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">$registry->load_registry_from_db(<o:p></o:p></p>
<p class="MsoNormal"> -host => 'ensembldb.ensembl.org',<o:p></o:p></p>
<p class="MsoNormal"> -user => 'anonymous',<o:p></o:p></p>
<p class="MsoNormal"> -verbose => 1<o:p></o:p></p>
<p class="MsoNormal">);<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">hangs, seemingly indefinitely. I checked and I can make a manual mysql connection to ensembldb.ensembl.org, but just doing a “show databases” took well over a minute to return:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">$ mysql -u anonymous -h ensembldb.ensembl.org<o:p></o:p></p>
<p class="MsoNormal">Welcome to the MariaDB monitor. Commands end with ; or \g.<o:p></o:p></p>
<p class="MsoNormal">Your MySQL connection id is 228387134<o:p></o:p></p>
<p class="MsoNormal">Server version: 5.6.33 MySQL Community Server (GPL)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">MySQL [(none)]> show databases;<o:p></o:p></p>
<p class="MsoNormal">…results appear…<br>
23330 rows in set (1 min 17.741 sec)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m guessing this is why the registry isn’t loading. Am I using the correct db still? Is anyone able to check why the performance is so slow or whether something is broken please.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Simon.<o:p></o:p></p>
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